RetrogeneDB ID: retro_eeur_175

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_147527:2539..2885(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RPL34
• Ensembl ID: ENSEEUG00000010390
• Aliases: None
• Description: ribosomal protein L34 [Source:HGNC Symbol;Acc:10340]

Sequence

>retro_eeur_175
GTGACATGCAAAGGTGGGCTGTCCTACAACTCAGCCTCTAACAAAACTAGACTGCCCTGAACTCCAGGTAATAGAGTCCT
TTACCTTAACATCAAGAAGGATGGGAAAGCCCTCAAGTCTGTATGTGATGTGTGCCCAGGCTGACTTTGAGGAGTTGGTG
CTGTGTGACCTAAAGTCATTAAGAGGCTAAGACAAGGAAAAAAAAAAAAAAGACATGTCAGTAGGACCTATGCTGAGTCA
TGTGTGCTAGGTGTGTCTGTGACAGAATCAAGTGCACTTTCTTACTGAGGAGGAGAAAATTGTCCTCAAAATATTGAGGG
CACAAGAACAAAGCCAAAAAACTAAA

Alignment

ORF - retro_eeur_175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.86 %
• Parental protein coverage: 96.58 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LTYRRRLSYNTASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGVCPGRLRGVRAVRPKVLKRLSK---TK
          .T....LSYN.ASNKTRL..TPGNR..YL..KK.GKA.KS.C.VCPG.L.GV.AV.PKV.KRL.......
Retrocopy VTCKGGLSYNSASNKTRLP*TPGNRVLYLNIKKDGKALKSVCDVCPG*L*GVGAV*PKVIKRLRQXXXXX

Parental  KHVSRAYGGS-MCAKCVRDRIKRAFLI-EEQKIVVKVLKAQAQSQKAK
          .HVSR.Y..S.MCA.CV.DRIK..FL..EE.KIV.K.L.AQ.QSQK.K
Retrocopy XHVSRTYAES<MCARCVCDRIKCTFLL<EEEKIVLKILRAQEQSQKTK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	48.50 RPM
SRP017611_kidney	0.00 RPM	125.84 RPM
SRP017611_liver	0.00 RPM	88.27 RPM

ChIP-Seq

Erinaceus europaeus was not studied using ChIP-Seq data.

EST

Erinaceus europaeus was not studied using EST data.

TSS

Erinaceus europaeus was not studied using FANTOM5 data.

Lab

retro_eeur_175 was not experimentally validated.

Homology

Retrocopy orthology:

Erinaceus europaeus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 118 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011179	26 retrocopies	retro_dnov_1172, retro_dnov_1775, retro_dnov_2020, retro_dnov_2025, retro_dnov_2079, retro_dnov_2127, retro_dnov_2137, retro_dnov_2275, retro_dnov_2385, retro_dnov_2501, retro_dnov_252, retro_dnov_262, retro_dnov_2627, retro_dnov_2651, retro_dnov_325, retro_dnov_339, retro_dnov_430, retro_dnov_553, retro_dnov_565, retro_dnov_59, retro_dnov_606, retro_dnov_635, retro_dnov_658, retro_dnov_862, retro_dnov_88, retro_dnov_978,
Erinaceus europaeus	ENSEEUG00000010390	5 retrocopies	retro_eeur_169, retro_eeur_175 , retro_eeur_373, retro_eeur_82, retro_eeur_89,
Gadus morhua	ENSGMOG00000009982	1 retrocopy	retro_gmor_31,
Loxodonta africana	ENSLAFG00000032615	6 retrocopies	retro_lafr_1039, retro_lafr_1232, retro_lafr_182, retro_lafr_298, retro_lafr_306, retro_lafr_733,
Macropus eugenii	ENSMEUG00000009361	3 retrocopies	retro_meug_1012, retro_meug_1754, retro_meug_1775,
Macaca mulatta	ENSMMUG00000011901	1 retrocopy	retro_mmul_162,
Monodelphis domestica	ENSMODG00000020601	3 retrocopies	retro_mdom_1690, retro_mdom_774, retro_mdom_836,
Mustela putorius furo	ENSMPUG00000008873	17 retrocopies	retro_mputfur_1028, retro_mputfur_1095, retro_mputfur_1130, retro_mputfur_1170, retro_mputfur_12, retro_mputfur_1242, retro_mputfur_1305, retro_mputfur_1480, retro_mputfur_1501, retro_mputfur_360, retro_mputfur_378, retro_mputfur_475, retro_mputfur_517, retro_mputfur_557, retro_mputfur_562, retro_mputfur_852, retro_mputfur_923,
Pongo abelii	ENSPPYG00000014988	18 retrocopies	retro_pabe_1171, retro_pabe_1351, retro_pabe_1609, retro_pabe_1630, retro_pabe_1859, retro_pabe_2338, retro_pabe_2560, retro_pabe_2784, retro_pabe_2931, retro_pabe_3330, retro_pabe_3352, retro_pabe_3375, retro_pabe_3788, retro_pabe_385, retro_pabe_420, retro_pabe_566, retro_pabe_77, retro_pabe_827,
Pelodiscus sinensis	ENSPSIG00000003295	1 retrocopy	retro_psin_60,
Sorex araneus	ENSSARG00000000177	8 retrocopies	retro_sara_111, retro_sara_218, retro_sara_411, retro_sara_538, retro_sara_565, retro_sara_591, retro_sara_645, retro_sara_726,
Sarcophilus harrisii	ENSSHAG00000001357	1 retrocopy	retro_shar_799,
Sarcophilus harrisii	ENSSHAG00000002052	3 retrocopies	retro_shar_131, retro_shar_324, retro_shar_419,
Tupaia belangeri	ENSTBEG00000003574	24 retrocopies	retro_tbel_1109, retro_tbel_1298, retro_tbel_1337, retro_tbel_1532, retro_tbel_1781, retro_tbel_1857, retro_tbel_1941, retro_tbel_213, retro_tbel_2162, retro_tbel_2165, retro_tbel_2372, retro_tbel_2391, retro_tbel_2601, retro_tbel_279, retro_tbel_335, retro_tbel_3606, retro_tbel_3984, retro_tbel_4059, retro_tbel_4398, retro_tbel_657, retro_tbel_74, retro_tbel_901, retro_tbel_974, retro_tbel_983,
Xenopus tropicalis	ENSXETG00000021095	1 retrocopy	retro_xtro_5,